FMO DATABASE

FMODB ID: 7GL1K

Calculation Name: 4IN3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4IN3

Chain ID: A

ChEMBL ID:

UniProt ID: Q05029

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	80
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-418303.530213
FMO2-HF: Nuclear repulsion	386979.43517
FMO2-HF: Total energy	-31324.095043
FMO2-MP2: Total energy	-31415.86693

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:-3:ASP)

Summations of interaction energy for fragment #1(A:-3:ASP)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
10.961	19.343	1.017	-3.867	-5.532	0.007

Interaction energy analysis for fragmet #1(A:-3:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.914 / q_NPA : -0.969

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	-1	GLU	-1	-0.873	-0.949	2.623	38.379	42.652	0.504	-1.967	-2.809	-0.003
4	A	0	PHE	0	-0.008	-0.007	2.616	-11.011	-7.248	0.513	-1.834	-2.443	0.010
5	A	1	MET	0	-0.051	-0.029	4.388	-8.703	-8.357	0.000	-0.066	-0.280	0.000
6	A	2	SER	0	-0.036	-0.012	6.559	-3.565	-3.565	0.000	0.000	0.000	0.000
7	A	3	SER	0	-0.032	0.004	6.715	-2.280	-2.280	0.000	0.000	0.000	0.000
8	A	4	VAL	0	-0.006	-0.002	8.721	-2.455	-2.455	0.000	0.000	0.000	0.000
9	A	5	ASP	-1	-0.923	-0.958	11.221	27.545	27.545	0.000	0.000	0.000	0.000
10	A	6	VAL	0	0.009	0.000	13.498	-1.429	-1.429	0.000	0.000	0.000	0.000
11	A	7	LEU	0	-0.016	-0.019	17.025	0.359	0.359	0.000	0.000	0.000	0.000
12	A	8	LEU	0	-0.007	-0.001	19.197	-0.490	-0.490	0.000	0.000	0.000	0.000
13	A	9	THR	0	-0.025	-0.010	22.425	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	10	VAL	0	-0.007	-0.012	24.963	-0.150	-0.150	0.000	0.000	0.000	0.000
15	A	11	GLY	0	0.037	0.025	27.182	-0.365	-0.365	0.000	0.000	0.000	0.000
16	A	12	LYS	1	0.929	0.948	30.579	-8.596	-8.596	0.000	0.000	0.000	0.000
17	A	13	LEU	0	-0.011	-0.003	29.176	0.226	0.226	0.000	0.000	0.000	0.000
18	A	14	ASP	-1	-0.880	-0.928	31.796	8.658	8.658	0.000	0.000	0.000	0.000
19	A	15	ALA	0	-0.031	-0.033	32.045	0.235	0.235	0.000	0.000	0.000	0.000
20	A	16	SER	0	-0.065	-0.018	31.137	0.396	0.396	0.000	0.000	0.000	0.000
21	A	17	LEU	0	0.011	0.000	28.538	0.382	0.382	0.000	0.000	0.000	0.000
22	A	18	ALA	0	0.033	0.022	26.489	-0.336	-0.336	0.000	0.000	0.000	0.000
23	A	19	LEU	0	-0.012	0.003	27.719	0.164	0.164	0.000	0.000	0.000	0.000
24	A	20	LEU	0	-0.036	-0.017	22.349	-0.032	-0.032	0.000	0.000	0.000	0.000
25	A	21	THR	0	0.031	0.013	26.163	-0.202	-0.202	0.000	0.000	0.000	0.000
26	A	22	THR	0	-0.015	-0.033	22.025	0.149	0.149	0.000	0.000	0.000	0.000
27	A	23	GLN	0	0.001	-0.017	24.008	-0.102	-0.102	0.000	0.000	0.000	0.000
28	A	24	ASP	-1	-0.873	-0.897	23.048	13.141	13.141	0.000	0.000	0.000	0.000
29	A	25	HIS	0	-0.050	-0.025	26.519	-0.239	-0.239	0.000	0.000	0.000	0.000
30	A	26	HIS	0	-0.018	0.007	23.525	-0.454	-0.454	0.000	0.000	0.000	0.000
31	A	27	VAL	0	-0.022	-0.028	26.690	0.014	0.014	0.000	0.000	0.000	0.000
32	A	28	ILE	0	-0.021	-0.011	21.830	-0.025	-0.025	0.000	0.000	0.000	0.000
33	A	29	GLU	-1	-0.911	-0.955	25.969	9.947	9.947	0.000	0.000	0.000	0.000
34	A	30	PHE	0	-0.010	-0.021	19.209	0.468	0.468	0.000	0.000	0.000	0.000
35	A	31	PRO	0	0.056	0.022	23.037	-0.453	-0.453	0.000	0.000	0.000	0.000
36	A	32	THR	0	0.037	0.009	24.317	0.575	0.575	0.000	0.000	0.000	0.000
37	A	33	VAL	0	-0.029	-0.010	24.614	0.142	0.142	0.000	0.000	0.000	0.000
38	A	34	LEU	0	-0.030	-0.014	19.682	0.286	0.286	0.000	0.000	0.000	0.000
39	A	35	LEU	0	-0.058	-0.006	20.448	0.793	0.793	0.000	0.000	0.000	0.000
40	A	36	PRO	0	-0.009	-0.014	19.590	-0.230	-0.230	0.000	0.000	0.000	0.000
41	A	37	GLU	-1	-0.877	-0.938	22.194	12.288	12.288	0.000	0.000	0.000	0.000
42	A	38	ASN	0	-0.043	-0.027	25.364	-0.727	-0.727	0.000	0.000	0.000	0.000
43	A	39	VAL	0	-0.038	-0.016	23.218	-0.310	-0.310	0.000	0.000	0.000	0.000
44	A	40	LYS	1	0.941	0.982	26.229	-10.297	-10.297	0.000	0.000	0.000	0.000
45	A	41	ALA	0	0.060	0.017	29.662	0.059	0.059	0.000	0.000	0.000	0.000
46	A	42	GLY	0	-0.025	-0.010	30.338	-0.168	-0.168	0.000	0.000	0.000	0.000
47	A	43	SER	0	-0.055	-0.018	26.192	0.007	0.007	0.000	0.000	0.000	0.000
48	A	44	ILE	0	0.007	0.006	22.177	0.038	0.038	0.000	0.000	0.000	0.000
49	A	45	ILE	0	0.000	0.007	19.779	0.244	0.244	0.000	0.000	0.000	0.000
50	A	46	LYS	1	0.944	0.973	13.464	-21.837	-21.837	0.000	0.000	0.000	0.000
51	A	47	MET	0	-0.028	-0.009	14.962	0.353	0.353	0.000	0.000	0.000	0.000
52	A	48	GLN	0	-0.010	-0.005	9.653	-0.941	-0.941	0.000	0.000	0.000	0.000
53	A	49	VAL	0	-0.006	0.001	10.601	0.953	0.953	0.000	0.000	0.000	0.000
54	A	50	SER	0	0.070	0.039	5.850	2.502	2.502	0.000	0.000	0.000	0.000
55	A	51	GLN	0	-0.032	-0.008	7.020	-2.608	-2.608	0.000	0.000	0.000	0.000
56	A	52	ASN	0	0.062	-0.004	6.835	3.853	3.853	0.000	0.000	0.000	0.000
57	A	53	LEU	0	0.061	0.041	6.850	-3.384	-3.384	0.000	0.000	0.000	0.000
58	A	54	GLU	-1	-1.031	-1.012	8.823	25.334	25.334	0.000	0.000	0.000	0.000
59	A	55	GLU	-1	-0.879	-0.965	10.427	17.451	17.451	0.000	0.000	0.000	0.000
60	A	56	GLU	-1	-0.844	-0.912	12.104	19.955	19.955	0.000	0.000	0.000	0.000
61	A	57	LYS	1	0.913	0.955	10.800	-25.021	-25.021	0.000	0.000	0.000	0.000
62	A	58	LYS	1	0.954	0.985	14.534	-20.403	-20.403	0.000	0.000	0.000	0.000
63	A	59	GLN	0	0.058	0.020	16.476	-1.686	-1.686	0.000	0.000	0.000	0.000
64	A	60	ARG	1	0.907	0.964	14.752	-18.360	-18.360	0.000	0.000	0.000	0.000
65	A	61	ASN	0	-0.030	-0.028	18.152	-1.249	-1.249	0.000	0.000	0.000	0.000
66	A	62	HIS	0	0.009	0.026	20.608	-0.519	-0.519	0.000	0.000	0.000	0.000
67	A	63	PHE	0	0.034	0.016	22.240	-0.697	-0.697	0.000	0.000	0.000	0.000
68	A	64	LYS	1	0.977	0.968	23.642	-12.649	-12.649	0.000	0.000	0.000	0.000
69	A	65	SER	0	-0.035	-0.003	25.107	-0.552	-0.552	0.000	0.000	0.000	0.000
70	A	66	ILE	0	0.036	0.019	26.548	-0.496	-0.496	0.000	0.000	0.000	0.000
71	A	67	GLN	0	-0.008	-0.012	28.225	-0.665	-0.665	0.000	0.000	0.000	0.000
72	A	68	ALA	0	-0.003	0.004	29.533	-0.358	-0.358	0.000	0.000	0.000	0.000
73	A	69	LYS	1	0.878	0.954	30.963	-9.232	-9.232	0.000	0.000	0.000	0.000
74	A	70	ILE	0	-0.051	-0.038	32.168	-0.342	-0.342	0.000	0.000	0.000	0.000
75	A	71	LEU	0	-0.020	-0.013	34.134	-0.238	-0.238	0.000	0.000	0.000	0.000
76	A	72	GLU	-1	-0.889	-0.933	35.012	8.494	8.494	0.000	0.000	0.000	0.000
77	A	73	LYS	1	0.848	0.937	36.506	-8.541	-8.541	0.000	0.000	0.000	0.000
78	A	74	TYR	0	0.002	-0.009	37.586	-0.140	-0.140	0.000	0.000	0.000	0.000
79	A	75	GLY	0	0.041	0.034	39.458	0.117	0.117	0.000	0.000	0.000	0.000
80	A	76	THR	0	-0.021	-0.010	40.536	-0.003	-0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-3:ASP)